Rapid-Thermal Annealing (RTA) with radiation heating is recently adopted in nanoscale CMOS fabrication in order to achieve ultra-shallow junction with maximum dopant activation rate. However, recent results report the systematic shift of threshold voltage (Vth) and increased Vth variation due to RTA process [1-2]. The exact amount of variations depends on layout pattern density, RTA heating temperature (T) and effective annealing time. In this work, we develop joint thermal/TCAD simulation and compact modeling tools to analyze performance variability under various layout pattern densities and RTA conditions. With the new simulation capability, we recognize two major variation mechanisms under RTA: the change of effective channel length (Leff) induced by lateral dopant diffusion, and the fluctuation of equivalent oxide thickness (EOT) due to incomplete dopant activation. We perform device simulations to quantify transistor performance shift due to L eff and EOT variations. Moreover, we propose a suite of compact models that bridge the underlying RTA process with device parameter change for efficient design optimization. The new tools are validated with published silicon data at 45nm and 65nm nodes. They will facilitate physical designers to predict and mitigate circuit performance variability due to the layout-dependent RTA process.